Atena Abedi Maghami , Ashraf Mohabati Mobarez , Abbas Yadegar , Maryam Nikkhah , Amir Sadeghi , Marziyeh Mousazadeh
{"title":"Evaluation of optimized Real time-PCR HRM assay and SPR-based biosensor for noninvasive isolation of H. pylori and Clarithromycin resistance 23S-SNP subtype","authors":"Atena Abedi Maghami , Ashraf Mohabati Mobarez , Abbas Yadegar , Maryam Nikkhah , Amir Sadeghi , Marziyeh Mousazadeh","doi":"10.1016/j.diagmicrobio.2025.116722","DOIUrl":"10.1016/j.diagmicrobio.2025.116722","url":null,"abstract":"<div><div>High Resolution Melting analysis is a highly sensitive molecular method, and the plasmonic-based sensor is a convenient test, be clinically elicited, in simultaneous <em>H. pylori</em> control and the prevention of Clarithromycin resistant strains related to SNPs. Comparing gold standard tests, we evaluated HRMA and the SPR-based biosensor in regard to noninvasive forms of <em>H. pylori</em> management, and explored resistance through a possible mechanism by 23S-SNPs.We optimized Realtime-PCR HRM analysis, and SPR-based biosensor. Referring to CTs ± 38, isolation sensitivity was evaluated at 74 %. Compared to the reference-test, results agreements were assessed with a kappa of 43 %, <em>p</em> = 0.001. Within melting plots (differentiation plot), the strains were detectable at Tms ranging from 81.5 to 82.3 (°C). Contributing to phenotypically determined resistant strains for 44 %, there was a wide distribution among resistant variants assessed through Tms of 82, 81.5, 82, 82.3, and 81.7 (°C). A2143C was the only mutation isolated at a specific Tm of 82.3°C; kappa = 8 %, <em>p</em> = 0.3. For sensing analysis, including 100 % specificity, this sensor type was associated with lower sensitivity of 49 %, kappa=19 %, <em>p</em> = 0. 01. For SNP, specificity, kappa value, and p-value of isolation were 100 %, 100 %, and 0.001. Lod was 0.003 ng/mL and 0.03 µg/mL for HRM assay and sensing analysis. In our evaluations, applicable priority of HRM analysis was the higher estimation of sensitivity; its differentiation plot was completely covered the results of strain variability regarding specific SNPs detection. Consistent with the biosensor for isolation of SNP, the development of biosensors is the necessity for noninvasive <em>H. pylori</em> detection.</div></div>","PeriodicalId":11329,"journal":{"name":"Diagnostic microbiology and infectious disease","volume":"111 4","pages":"Article 116722"},"PeriodicalIF":2.1,"publicationDate":"2025-02-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143284138","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"A rare case of community-acquired hypervirulent Acinetobacter Pittii infection, study of molecular characteristics, and literature review","authors":"Jian Sun , Wenzeng Xu , Xiaoying Zhan , Xin Tian , Yunsong Yu","doi":"10.1016/j.diagmicrobio.2024.116564","DOIUrl":"10.1016/j.diagmicrobio.2024.116564","url":null,"abstract":"<div><h3>Background</h3><div><em>Acinetobacter pittii</em>, is typically a nosocomial pathogen and is rarely community-acquired.</div></div><div><h3>Case Presentation</h3><div>A 50-year-old male in China developed septic shock, multiorgan failure, and severe pneumonia. Cultures confirmed <em>A. pittii</em>, resistant to piperacillin-tazobactam but susceptible to other antibiotics. He recovered after 43 days of treatment.</div></div><div><h3>Conclusions</h3><div>Genome sequencing revealed high virulence, confirmed by larvicidal assays. This first report of community-acquired <em>A. pittii</em> highlights its potential for severe infections and septic shock, necessitating clinician awareness.</div></div>","PeriodicalId":11329,"journal":{"name":"Diagnostic microbiology and infectious disease","volume":"111 2","pages":"Article 116564"},"PeriodicalIF":2.1,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142738789","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Kyriaki Dimaka , Theodoros Karampatakis , Melina Kachrimanidou , Helen Katsifa , Maria Exindari
{"title":"Epidemiology of bacterial respiratory tract infections during the pre-pandemic, COVID-19 pandemic and post-pandemic era: A retrospective study of hospitalized adults in northern Greece between 2018 and 2023","authors":"Kyriaki Dimaka , Theodoros Karampatakis , Melina Kachrimanidou , Helen Katsifa , Maria Exindari","doi":"10.1016/j.diagmicrobio.2025.116710","DOIUrl":"10.1016/j.diagmicrobio.2025.116710","url":null,"abstract":"<div><h3>Introduction</h3><div>The COVID-19 pandemic has had impact on global healthcare and respiratory disease patterns. The aim was to evaluate the changes in positive respiratory cultures during the pandemic.</div></div><div><h3>Methods</h3><div>A retrospective analysis of respiratory specimens in Papanikolaou Hospital during 2018–2023 was performed. In total, 18,852 samples (12,277 males, 6575 females) of respiratory samples were recorded.</div></div><div><h3>Results</h3><div>During 2018–2019, 684 BAL samples were received, of which 12.3 % were positive. Positive pharyngeal smears constituted 24.8 %, compared to 18.5 % in pandemic years, and 29.6 % in 2023. In PTC, pre-pandemic, positives were 12.3 %, while in 2021 the maximum percentage of positives (21.9 %) was observed. Positive levels remained high in 2023 (18.3 %). Concerning bronchial secretions, there was an increase (55.3 % in 2022 vs 47.0 % in 2019). The predominant bacteria were <em>Acinetobacter spp, Klebsiella spp</em> and <em>Pseudomonas spp</em>.</div></div><div><h3>Conclusion</h3><div>Except for the bronchial secretions, the rest of the respiratory specimens do not exhibit any definite trends.</div></div>","PeriodicalId":11329,"journal":{"name":"Diagnostic microbiology and infectious disease","volume":"111 3","pages":"Article 116710"},"PeriodicalIF":2.1,"publicationDate":"2025-01-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143073522","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Murtaza Öz , Fatih Çubuk , Yasemin Çakır Kıymaz , Caner Öksüz , Mürşit Hasbek , Seyit Ali Büyüktuna , Nazif Elaldı
{"title":"Hidden threats: Brucellosis diagnosis and co-infection patterns in Crimean-Congo Hemorrhagic Fever suspects","authors":"Murtaza Öz , Fatih Çubuk , Yasemin Çakır Kıymaz , Caner Öksüz , Mürşit Hasbek , Seyit Ali Büyüktuna , Nazif Elaldı","doi":"10.1016/j.diagmicrobio.2025.116724","DOIUrl":"10.1016/j.diagmicrobio.2025.116724","url":null,"abstract":"<div><h3>Purpose</h3><div>This study aims to investigate the frequency of brucellosis in patients with Crimean-Congo Hemorrhagic Fever (CCHF).</div></div><div><h3>Method</h3><div>In this study, 1231 patients were evaluated retrospectively, including 14 patients with CCHF and brucellosis coinfection and 25 patients with brucellosis alone. Statistical methods such as the Mann-Whitney U test and Fisher's exact test were used.</div></div><div><h3>Result</h3><div>Of the patients with a preliminary diagnosis of Crimean-Congo Hemorrhagic Fever (CCHF), 3.2% were found to have brucellosis. In the group co-infected with brucellosis and CCHF, the time to hospital admission was shorter. Additionally, tick exposure and headache were observed more frequently in this group. Creatine kinase levels were found to be higher in the co-infected group, while lymphocyte counts and fibrinogen levels were lower compared to the group with brucellosis alone.</div></div><div><h3>Conclusion</h3><div>Our study revealed a 3.2% rate of brucellosis in patients with a preliminary diagnosis of CCHF. Due to the similarity of symptoms and common risk factors, the differential diagnosis of brucellosis should be considered in patients diagnosed with CCHF. Additionally, the possibility of brucellosis coexisting with CCHF should always be considered. Even in patients diagnosed with CCHF, an evaluation for brucellosis must be conducted.</div></div>","PeriodicalId":11329,"journal":{"name":"Diagnostic microbiology and infectious disease","volume":"111 3","pages":"Article 116724"},"PeriodicalIF":2.1,"publicationDate":"2025-01-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143167292","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Wentao Gu , Jing Wang , Xiaohua Qin , Meilin Duan , Minggui Wang , Yuanlin Guan , Xiaogang Xu
{"title":"The performance of nanopore sequencing in rapid detection of pathogens and antimicrobial resistance genes in blood cultures","authors":"Wentao Gu , Jing Wang , Xiaohua Qin , Meilin Duan , Minggui Wang , Yuanlin Guan , Xiaogang Xu","doi":"10.1016/j.diagmicrobio.2025.116720","DOIUrl":"10.1016/j.diagmicrobio.2025.116720","url":null,"abstract":"<div><div>Rapid identification of causative microbes and their resistance is essential for effective monitoring, treating, and controlling of infectious diseases. Oxford Nanopore Technologies (ONT) is capable of generating and analyzing data in real time, its potential in clinically detecting pathogens and antimicrobial resistance (AMR) genes and subsequently predicting resistance phenotypes needs to be evaluated. In this study, positive blood cultures from 67 patients with bloodstream infection were collected for matrix-assisted laser desorption ionization–time of flight mass spectrometry (MALDI-TOF-MS), ONT next generation sequencing (NGS) with a sequencing time limit of 1 h, and Illumina NGS. Antimicrobial susceptibility test was also performed. ONT NGS achieved 100 % coincidence rate (67/67) with MALDI-TOF-MS and Illumina NGS in pathogen identification, the sensitivity reached 100 %. Both ONT and Illumina NGS detected a high number of AMR genes (584 and 585, respectively). The consistent rate of ONT NGS against Illumina NGS for AMR genes detection reached 91.79 % (537/585). When considering antimicrobial susceptibility test results as the standard to evaluate the prediction value of ONT NGS in detecting AMR genes, ONT NGS showed competitive sensitivity (77.4 % vs 77.3 %), specificity (83.3 % vs 83.7 %), and accuracy (80.4 % vs 80.4 %) with Illumina NGS. Furthermore, the average time cost of ONT NGS (3.5 h) was significantly shorter than Illumina NGS (50.5 h) and MALDI-TOF-MS + antimicrobial susceptibility test (66-96 h). These findings highlight the potential of ONT NGS in rapidly and accurately detecting pathogens and AMR genes in clinical practices, which can assist in predicting resistance phenotypes and subsequently improving the diagnosis and treatment of infectious diseases.</div></div>","PeriodicalId":11329,"journal":{"name":"Diagnostic microbiology and infectious disease","volume":"111 3","pages":"Article 116720"},"PeriodicalIF":2.1,"publicationDate":"2025-01-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143122428","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Begoña de Escalante Yangüela , Jorge Ligero López , Alejandro Venegas Robles , Rosana Urdaniz Borque , Juan Vallejo Grijalba , Orosia Bandrés Nivela , José Luis Juan Bañón , Antonio Beltrán Rosel
{"title":"Successful maintenance therapy with moxifloxacin for disseminated nocardiosis caused by Nocardia farcinica in a patient with Cushing's syndrome","authors":"Begoña de Escalante Yangüela , Jorge Ligero López , Alejandro Venegas Robles , Rosana Urdaniz Borque , Juan Vallejo Grijalba , Orosia Bandrés Nivela , José Luis Juan Bañón , Antonio Beltrán Rosel","doi":"10.1016/j.diagmicrobio.2025.116718","DOIUrl":"10.1016/j.diagmicrobio.2025.116718","url":null,"abstract":"<div><div><em>Nocardia</em> species are aerobic, Gram-positive actinomycetes often causing opportunistic infections, particularly in immunocompromised hosts. <em>Nocardia farcinica</em> is notable for disseminated nocardiosis (DN), frequently involving the lungs and central nervous system (CNS). Cushing's syndrome (CS), characterized by hypercortisolemia, further predisposes patients to severe infections.</div><div>We report a 73-year-old woman with ACTH-dependent CS due to a pituitary adenoma who developed DN with pleuropulmonary, CNS, and gluteal abscesses. Diagnosis was confirmed through cultures and MALDI-TOF MS, identifying <em>N. farcinica</em>. Resistance to standard antibiotics required a tailored regimen, including imipenem, amikacin, and moxifloxacin, alongside surgical management of abscesses and the adenoma.</div><div>This case emphasizes the importance of rapid diagnostic methods and individualized therapies in managing DN with CS, a rare but severe combination. It highlights the need for vigilance in high-risk patients and contributes valuable insights for optimizing outcomes in such complex cases.</div></div>","PeriodicalId":11329,"journal":{"name":"Diagnostic microbiology and infectious disease","volume":"111 3","pages":"Article 116718"},"PeriodicalIF":2.1,"publicationDate":"2025-01-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143167301","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Sofía Cano , María Ángeles Clari , Eliseo Albert , Elena Villar , Beatriz Quevedo Sánchez , Nieves Carbonell , David Navarro
{"title":"Detection rate of herpes simplex virus DNA in the lower respiratory tract of critical care patients with or without coinfection determined by the Biofire® pneumonia plus panel","authors":"Sofía Cano , María Ángeles Clari , Eliseo Albert , Elena Villar , Beatriz Quevedo Sánchez , Nieves Carbonell , David Navarro","doi":"10.1016/j.diagmicrobio.2025.116721","DOIUrl":"10.1016/j.diagmicrobio.2025.116721","url":null,"abstract":"<div><div>We investigated whether the results returned by the Biofire® Pneumonia Plus Panel (FA-PP) in lower respiratory tract specimens (LRT) specimens may identify patients who should be targeted for Herpes simplex virus (HSV) DNA testing. We included 35 adult ICU patients who underwent protocolized HSV DNA testing in LRT and/or plasma specimens by real-time PCR. Of these, one patient underwent allogeneic hematopoietic cell transplantation, one a kidney transplantation and one was under CAR-T cell therapy. Twenty-three of the 33 patients (69.6 %) had HSV-type 1 (HSV-1) DNA detected in LRT specimens (median viral load: 5.67 log<sub>10</sub> copies/ml). Viral DNA was detected in 12/14 (85 %) plasma samples (median, 3.4 log<sub>10</sub> copies/ml) from patients with HSV-1 DNA present in LRT specimens. Patients testing positive by the FA-PP had a non-significant (<em>P</em> = 0.28) higher rate of HSV-1 DNA detection (10/13; 77 %) compared with patients returning negative results (9/16; 56 %). In conclusion, requests for HSV DNA testing in ICU patients should not depend on the results of conventional culture methods nor those provided by the FA-PP.</div></div>","PeriodicalId":11329,"journal":{"name":"Diagnostic microbiology and infectious disease","volume":"111 3","pages":"Article 116721"},"PeriodicalIF":2.1,"publicationDate":"2025-01-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143073521","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Prevalence and genetic insights of linezolid resistance in tuberculosis: A study of sensitive and resistant clinical isolates","authors":"Mina Hajizadeh , Niloofar Hekmatpour , Bahman Rahimlou , Alireza Eskandari , Mohammad Saber Zamani , Kianoosh Ferdosnejad , Fatemeh Sakhaee , Morteza Masoumi , Majid Marjani , Samira Tarashi , Seyed Davar Siadat","doi":"10.1016/j.diagmicrobio.2025.116719","DOIUrl":"10.1016/j.diagmicrobio.2025.116719","url":null,"abstract":"<div><div>Despite undiagnosed tuberculosis cases, it remains a major global health issue, complicated by antibiotic resistance. Linezolid has been approved for multidrug-resistant (MDR) TB management, but data on its resistance in clinical isolates is limited. This research aims to assess linezolid resistance and identify associated mutations in both sensitive and MDR tuberculosis isolates. The minimum inhibitory concentration (MIC) of linezolid was assessed for 60 isolates, including 40 sensitive and 20 MDR strains, using the broth microdilution method. Additionally, the <em>rplC</em> and <em>rrl</em> genes associated with linezolid resistance was sequenced. Resistance to linezolid was detected in 4 out of the 60 isolates (6.6 %), which included one sensitive strain (2.5 %) and three MDR tuberculosis strains (15 %). The MIC values were found to be 4 µg/ml for sensitive isolates, and 16 µg/ml (<em>n</em> = 1) and 8 µg/ml (<em>n</em> = 2) for the MDR strains. The A297T mutation was detected in one MDR tuberculosis isolate exhibiting linezolid resistance, while no mutations were observed in the <em>rrl</em> gene. Generally, the incidence of linezolid-resistant isolates among tuberculosis cases is 6.6 %, highlighting the necessity of drug susceptibility testing for linezolid in managing complex drug-resistant infections. Further research is required to investigate additional genetic resistance mechanisms in tuberculosis.</div></div>","PeriodicalId":11329,"journal":{"name":"Diagnostic microbiology and infectious disease","volume":"111 3","pages":"Article 116719"},"PeriodicalIF":2.1,"publicationDate":"2025-01-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143122413","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Raimond Lugert, Yvonne Laukat, Sabine Rabenda, Michael Weig, Uwe Groß, Wolfgang Bohne
{"title":"Evaluation of the DiaSorin NxTAG gastrointestinal pathogen panel (GPP) and its integration into routine diagnostics","authors":"Raimond Lugert, Yvonne Laukat, Sabine Rabenda, Michael Weig, Uwe Groß, Wolfgang Bohne","doi":"10.1016/j.diagmicrobio.2025.116717","DOIUrl":"10.1016/j.diagmicrobio.2025.116717","url":null,"abstract":"<div><div>This study evaluated the performance of the DiaSorin NxTAG GPP multiplex PCR system, the advanced successor of the Luminex-xTAG-GPP, in comparison to classical diagnostic techniques for stool samples. In a testing phase, we investigated 505 specimens using both the DiaSorin system and our conventional approach consisting of culture techniques, PCR detection and microscopic analysis. The multiplex PCR system proved to be superior in sensitivity, time efficiency, and pathogen range. The analysis of 2,462 stool samples after the system's implementation into routine diagnostics further confirmed its effectiveness. However, we encountered several <em>Salmonella</em>-positive samples, which could neither be confirmed by culture techniques nor by an independently performed <em>Salmonella</em>-specific PCR. This let us to permanently incorporate a confirmatory PCR assay for <em>Salmonella</em>-positive samples, in order to avoid false positives. Our findings indicate that the DiaSorin NxTAG GPP is a reliable and efficient diagnostic tool for most gastrointestinal pathogens, with the exception of <em>Salmonella</em>.</div></div>","PeriodicalId":11329,"journal":{"name":"Diagnostic microbiology and infectious disease","volume":"111 3","pages":"Article 116717"},"PeriodicalIF":2.1,"publicationDate":"2025-01-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143078892","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}